I just encountered the same issue. The main reason seems to be a hard-coded setting in the bootstrap3 plugin.
To make it work with the Cloudron-packaged app:
- add the path
/app/code
to the$doku_inc_dirs
array intemplates/bootstrap3/css.php
andtemplates/bootstrap3/iconify.php
- when setting the theme through the DokuWiki Admin panel, the following setting is added to
/conf/local.php
: